DP2L_THEKO
ID DP2L_THEKO Reviewed; 1798 AA.
AC Q5JET0;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 110.
DE RecName: Full=DNA polymerase II large subunit;
DE Short=Pol II;
DE EC=2.7.7.7 {ECO:0000255|HAMAP-Rule:MF_00324};
DE AltName: Full=Exodeoxyribonuclease large subunit {ECO:0000255|HAMAP-Rule:MF_00324};
DE EC=3.1.11.1 {ECO:0000255|HAMAP-Rule:MF_00324};
DE Contains:
DE RecName: Full=Pko polC intein;
DE AltName: Full=Pko pol II intein;
GN Name=polC; OrderedLocusNames=TK1903;
OS Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
OS (Pyrococcus kodakaraensis (strain KOD1)).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Thermococcus.
OX NCBI_TaxID=69014;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=15710748; DOI=10.1101/gr.3003105;
RA Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.;
RT "Complete genome sequence of the hyperthermophilic archaeon Thermococcus
RT kodakaraensis KOD1 and comparison with Pyrococcus genomes.";
RL Genome Res. 15:352-363(2005).
CC -!- FUNCTION: Possesses two activities: a DNA synthesis (polymerase) and an
CC exonucleolytic activity that degrades single-stranded DNA in the 3'- to
CC 5'-direction. Has a template-primer preference which is characteristic
CC of a replicative DNA polymerase (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC ChEBI:CHEBI:173112; EC=2.7.7.7;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage in the 3'- to 5'-direction to yield
CC nucleoside 5'-phosphates.; EC=3.1.11.1; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00324};
CC -!- SUBUNIT: Heterodimer of a large subunit and a small subunit.
CC {ECO:0000250}.
CC -!- PTM: This protein undergoes a protein self splicing that involves a
CC post-translational excision of the intervening region (intein) followed
CC by peptide ligation. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the archaeal DNA polymerase II family.
CC {ECO:0000305}.
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DR EMBL; AP006878; BAD86092.1; -; Genomic_DNA.
DR RefSeq; WP_011250854.1; NC_006624.1.
DR PDB; 6KNB; EM; 6.90 A; B=1-1798.
DR PDB; 6KNC; EM; 9.30 A; B=1-1798.
DR PDBsum; 6KNB; -.
DR PDBsum; 6KNC; -.
DR AlphaFoldDB; Q5JET0; -.
DR SMR; Q5JET0; -.
DR STRING; 69014.TK1903; -.
DR MEROPS; N10.005; -.
DR PRIDE; Q5JET0; -.
DR EnsemblBacteria; BAD86092; BAD86092; TK1903.
DR GeneID; 3233964; -.
DR KEGG; tko:TK1903; -.
DR PATRIC; fig|69014.16.peg.1861; -.
DR eggNOG; arCOG03145; Archaea.
DR eggNOG; arCOG04447; Archaea.
DR HOGENOM; CLU_001154_0_0_2; -.
DR InParanoid; Q5JET0; -.
DR OMA; KRRNCDG; -.
DR OrthoDB; 559at2157; -.
DR PhylomeDB; Q5JET0; -.
DR Proteomes; UP000000536; Chromosome.
DR GO; GO:0008408; F:3'-5' exonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0008852; F:exodeoxyribonuclease I activity; IEA:UniProtKB-EC.
DR GO; GO:0000738; P:DNA catabolic process, exonucleolytic; IEA:UniProtKB-UniRule.
DR GO; GO:0006261; P:DNA-templated DNA replication; IEA:UniProtKB-UniRule.
DR GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
DR GO; GO:0006314; P:intron homing; IEA:UniProtKB-KW.
DR Gene3D; 3.10.28.10; -; 1.
DR HAMAP; MF_00324; DNApol_II_L_arch; 1.
DR InterPro; IPR003586; Hint_dom_C.
DR InterPro; IPR003587; Hint_dom_N.
DR InterPro; IPR036844; Hint_dom_sf.
DR InterPro; IPR027434; Homing_endonucl.
DR InterPro; IPR006142; INTEIN.
DR InterPro; IPR030934; Intein_C.
DR InterPro; IPR004042; Intein_endonuc.
DR InterPro; IPR006141; Intein_N.
DR InterPro; IPR004860; LAGLIDADG_2.
DR InterPro; IPR004475; PolC_DP2.
DR InterPro; IPR016033; PolC_DP2_N.
DR PANTHER; PTHR42210; PTHR42210; 1.
DR Pfam; PF14528; LAGLIDADG_3; 1.
DR Pfam; PF03833; PolC_DP2; 1.
DR PRINTS; PR00379; INTEIN.
DR SMART; SM00305; HintC; 1.
DR SMART; SM00306; HintN; 1.
DR SUPFAM; SSF51294; SSF51294; 1.
DR SUPFAM; SSF55608; SSF55608; 1.
DR TIGRFAMs; TIGR01445; intein_Nterm; 1.
DR TIGRFAMs; TIGR00354; polC; 1.
DR PROSITE; PS50818; INTEIN_C_TER; 1.
DR PROSITE; PS50819; INTEIN_ENDONUCLEASE; 1.
DR PROSITE; PS50817; INTEIN_N_TER; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Autocatalytic cleavage; DNA replication; DNA-binding;
KW DNA-directed DNA polymerase; Endonuclease; Exonuclease; Hydrolase;
KW Intron homing; Multifunctional enzyme; Nuclease; Nucleotidyltransferase;
KW Protein splicing; Reference proteome; Transferase.
FT CHAIN 1..963
FT /note="DNA polymerase II large subunit, 1st part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000007310"
FT CHAIN 964..1437
FT /note="Pko polC intein"
FT /evidence="ECO:0000255"
FT /id="PRO_0000007311"
FT CHAIN 1438..1798
FT /note="DNA polymerase II large subunit, 2nd part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000007312"
FT DOMAIN 1184..1319
FT /note="DOD-type homing endonuclease"
FT REGION 286..309
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1699..1798
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1733..1754
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1774..1792
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 1798 AA; 204935 MW; 60960A04B7BFAFAE CRC64;
MSEEIYSPEM KAYFESLQRE IDRAYAIARK ARAQGKDPSF DVEVPQATDM AGRVESLVGP
PGVAERIREL VKEYGKEIAA LKVVDEIIEG KFGDLGSKEK YAEQAVRTAL AILTEGIVSA
PLEGIADVKI KRNEWADGSE YLALYYAGPI RSSGGTAQAL SVLVGDYVRR KLGLDRFKPS
DEHIERMVEE VDLYHRAVTR LQYHPEADEV RLAMRNIPIE ITGEETDKVE VSHRNVPGVE
TNHLRGGAIL VLAEGVLQKA KKLVKYIDKM GIEGWDWIKE FVEAKEKGKS SEENKDESKA
EDTGTESVAE KKENVEKGFY YELYEKFRAN IAPNKKYTKE IIGGRPLFAE PSTNGGFRLR
YGRSRVSGFA TWSVNPATML ILDEFIAIGT QMKTERPGKG CIVTPATTVE GPIVRLKNGS
VVRVDDYETA LKVRNEVDEI LYVGDALVNF GDFVENNQTL LPANYVEEWW VQELVQAIKD
LYEVELQPFA ENDREAVEEA AEYLEVDPDF LWNLLKDPLR VKPDVETAIH LSTVLDIPFH
PYYTLYWNTL QPEEVEELQK ALLGAQIEWA EFRKNRFAKK VVLENDKNIK RYLELLGLPH
RLERVEKKRK VIVVEYPWSA ALLTPLGNLE WEFKAKPFYT VIDIINENNR IKLRDRGISW
IGARMGRPEK AKERKMKPPV QVLFPIGLAG GQSRDIKKAA EEGKTARVEI AFFKCPKCGH
VGPEHLCPVC GTRKELLWHC PKCGADYPES DAKDFNYRCP KCDVELKPYA EREIKPADLL
RQAMDNVKVY GIDRLKGVKG MTSGYKMAEP LEKGLLRVKN DVYVFKDGTI RFDATDAPIT
HFKPKEIGTS VEKLRELGYT HDFEGKPLER DDQILELKVQ DVILPYEAGR YLLKVARFID
DLLEKFYGLP RFYNAEKMED LVGHLVIGLA PHTSAGIIGR IIGFSDVLVG YAHPYYHAAK
RRNCFPGDTR ILVQINGLPQ RITLRELYDL FEDERYENMA YVRKKPKADV KVYSFDPESG
KVVLTDIEDV IKAPSTDHLI RFELELGRSF ETTVDHPVLV YENGKFVEKR AFEVREGDRI
LVPNLKLPEK NIDYLDLLKE FSREEFAHLH DRIMVRGIAE WLRSVEADVK EDYLRRDSIP
LSVLLRVLTE KEISIEEVPS CWLGFKRDKV RIKRFVPLKP LLRVVGYYLA EGYARESKSV
YQLSFSMAEK EVREDLKRAL REAFGDGFGI YERGGKVTVG SRILYLLFTE VLKAGKNAYS
KRVPSLVFTL PREAVAEMLK AYFEGDGSAL KSVPRVVAYS VNKALLEDIE TLLLAKFGIR
GYYTFDNNAN RGNARGRLYH VERGTEAPVS KVYALNIAGE HYHRFFNSIG FVSERKNSIY
ELHAEKSPAQ DRYSSQNGWL VKVRRIEYIT PKDDFVFSLN AKKYHNVIIN ESIVTHQCDG
DEDAVMLLLD ALLNFSKYYL PEKRGGKMDA PLVVTTRLDP REVDSEVHNM DVVRYYPLEF
YKATYELKSP KEVKVIERVE DRLGKPEMYE GIKFTHDTDD IGLGPKMSLY KQLGDMEEKV
ARQLALAERI RAVDEHHVAE TIINSHLVPD LRGNLRSFTR QEFRCVKCNT KYRRPPLTGK
CPKCGGKIVL TVSKGAIEKY LPTAKMLVTK YRVKDYTRQR ICITEKDIKT LFENVFPEKQ
RTLMGFSADI CEKMVKERTG HSNGKNGYLD EFNGKNGKAS KKSGSLASKL SGKGKEPSKK
KESAKPKRSE KVKNLTSFEA AAKNEQARGT AGNAKKAESE KPKRKKRKGI SLDEFFGS
